You'd likely want to review the eMMC specification documents thoroughly to understand the differences. If you are dependent on third part code check if reads the version of the card, and applies different methods accordingly.

FATFS is agnostic to the block storage media being used, you get to manage any behaviour specific to the media in the DISKIO layer.

Is it like only these 6 API functions - disk_initialize, disk_status, disk_read, disk_write, disk_ioctl, get_fattime needs to be rewritten for the new JEDEC v5.0 specificication? or something else as well?